AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00480_ctra_reg_300.orf -o00480_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.41
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	zwf	300	Glucose-6-P Dehyrogenase

Motif number 1

AAGAGAGAGCCCACAATACCAAAAAAACGA	1	46	0	CCACAATACC	    0.996982	-255
TTAATTTCTTCCAAGATACAACCTAGTATA	1	91	0	CCAAGATACA	    0.988115	-210
GACTTTGGCCCCACATTACCAGCCTGTCCT	1	122	1	CCACATTACC	    0.992409	-179
CCAAAAATAACCACGATACAGGGAGGACAG	1	145	0	CCACGATACA	    0.996982	-156
          **********

Masking position 7
Map Score:   7.14259

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 7
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 2

AAAAAGATTTCTCTCTCATAAAACA     	1	6	0	CTCTCTCATA	    0.960805	-295
GTATTGTGGGCTCTCTCTTAAAAAATTAAC	1	57	1	CTCTCTCTTA	    0.932893	-244
AAAATTAACACTCTATACTAGGTTGTATCT	1	78	1	CTCTATACTA	    0.930008	-223
TGGGGCCAAAGTCTTTAATTTCTTCCAAGA	1	105	0	GTCTTTAATT	    0.783771	-196
TTACCAGCCTGTCCTCCCTGTATCGTGGTT	1	137	1	GTCCTCCCTG	    0.931107	-164
CTCTAGGAAGCTCTTTCCTGCTTTATACAA	1	193	1	CTCTTTCCTG	    0.988994	-108
TCGGATAGACGTCCTTCCTTTGTTAAATTG	1	220	0	GTCCTTCCTT	    0.970498	-81
AAGGAAGGACGTCTATCCGAAAACTTTGTT	1	230	1	GTCTATCCGA	    0.939135	-71
          **********

Masking position 2
Map Score:   4.8915

Number of sites scoring better than the average of aligned sites = 482
Number in coding regions = 482
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

AAGATTTCTCTCTCATAAAACA          	1	1	0	TCTCTAAACA	    0.968802	-300
GAGAGAGAAATCTTTTTAGGCACATATTCGTT	1	19	1	TCTTTTAGCA	    0.948054	-282
TTGTGGGCTCTCTCTTAAAAAATTAACACTCT	1	60	1	TCTCTAAAAA	    0.911043	-241
CTAGGTTGTATCTTGGAAGAAATTAAAGACTT	1	95	1	TCTTGAAGAA	    0.914589	-206
AGAGGTCAAGTCTCCTGTAGCACCAAAAATAA	1	165	0	TCTCTGTACA	    0.958868	-136
GCGACCTAAGTCTCATGAGCAATTTCGCGAAG	1	277	1	TCTCTGAGAA	    0.989355	-24
          **** **** **

Masking position 3
Map Score:   2.97749

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 148
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

TAGGCACATATTCGTTTTTTTGGTATTGTG	1	35	1	TTCGTTTTTT	    0.969645	-266
GTATAGAGTGTTAATTTTTTAAGAGAGAGC	1	66	0	TTAATTTTTT	    0.950323	-235
GCCAAAGTCTTTAATTTCTTCCAAGATACA	1	101	0	TTAATTTCTT	    0.918176	-200
CTGTATCGTGGTTATTTTTGGTGCTACAGG	1	154	1	GTTATTTTTG	    0.852921	-147
ATAGACGTCCTTCCTTTGTTAAATTGTATA	1	216	0	TTCCTTTGTT	    0.949335	-85
ATCCGAAAACTTTGTTTGTGTTGGGTTTGC	1	244	1	TTTGTTTGTG	     0.94867	-57
          **********

Masking position 5
Map Score:   1.02666

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 314
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 7

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0